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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: X-153804122-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153804122&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153804122,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001303512.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1559C>G",
"hgvs_p": "p.Pro520Arg",
"transcript": "NM_001303512.2",
"protein_id": "NP_001290441.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 775,
"cds_start": 1559,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 3761,
"mane_select": "ENST00000393758.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303512.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1559C>G",
"hgvs_p": "p.Pro520Arg",
"transcript": "ENST00000393758.7",
"protein_id": "ENSP00000377355.3",
"transcript_support_level": 1,
"aa_start": 520,
"aa_end": null,
"aa_length": 775,
"cds_start": 1559,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 3761,
"mane_select": "NM_001303512.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393758.7"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1541C>G",
"hgvs_p": "p.Pro514Arg",
"transcript": "ENST00000164640.8",
"protein_id": "ENSP00000164640.4",
"transcript_support_level": 1,
"aa_start": 514,
"aa_end": null,
"aa_length": 769,
"cds_start": 1541,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1733,
"cdna_end": null,
"cdna_length": 3689,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000164640.8"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1214C>G",
"hgvs_p": "p.Pro405Arg",
"transcript": "ENST00000544474.5",
"protein_id": "ENSP00000442033.1",
"transcript_support_level": 1,
"aa_start": 405,
"aa_end": null,
"aa_length": 660,
"cds_start": 1214,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 1464,
"cdna_end": null,
"cdna_length": 3418,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544474.5"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1556C>G",
"hgvs_p": "p.Pro519Arg",
"transcript": "ENST00000933007.1",
"protein_id": "ENSP00000603066.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 774,
"cds_start": 1556,
"cds_end": null,
"cds_length": 2325,
"cdna_start": 2188,
"cdna_end": null,
"cdna_length": 4144,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933007.1"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1541C>G",
"hgvs_p": "p.Pro514Arg",
"transcript": "NM_032512.5",
"protein_id": "NP_115901.2",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 769,
"cds_start": 1541,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1787,
"cdna_end": null,
"cdna_length": 3743,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032512.5"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1316C>G",
"hgvs_p": "p.Pro439Arg",
"transcript": "NM_001303515.2",
"protein_id": "NP_001290444.1",
"transcript_support_level": null,
"aa_start": 439,
"aa_end": null,
"aa_length": 694,
"cds_start": 1316,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 1726,
"cdna_end": null,
"cdna_length": 3682,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303515.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1298C>G",
"hgvs_p": "p.Pro433Arg",
"transcript": "NM_001303516.2",
"protein_id": "NP_001290445.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 688,
"cds_start": 1298,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 1708,
"cdna_end": null,
"cdna_length": 3664,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303516.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1298C>G",
"hgvs_p": "p.Pro433Arg",
"transcript": "ENST00000933008.1",
"protein_id": "ENSP00000603067.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 688,
"cds_start": 1298,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 1402,
"cdna_end": null,
"cdna_length": 3358,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933008.1"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1253C>G",
"hgvs_p": "p.Pro418Arg",
"transcript": "NM_001303513.3",
"protein_id": "NP_001290442.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 673,
"cds_start": 1253,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 2048,
"cdna_end": null,
"cdna_length": 4004,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303513.3"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1214C>G",
"hgvs_p": "p.Pro405Arg",
"transcript": "NM_001303514.2",
"protein_id": "NP_001290443.1",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 660,
"cds_start": 1214,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 1460,
"cdna_end": null,
"cdna_length": 3416,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303514.2"
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.1115C>G",
"hgvs_p": "p.Pro372Arg",
"transcript": "ENST00000933009.1",
"protein_id": "ENSP00000603068.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 627,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 1188,
"cdna_end": null,
"cdna_length": 3144,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933009.1"
}
],
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"dbsnp": "rs544558369",
"frequency_reference_population": 0.0002085803,
"hom_count_reference_population": 69,
"allele_count_reference_population": 240,
"gnomad_exomes_af": 0.000165833,
"gnomad_genomes_af": 0.000599409,
"gnomad_exomes_ac": 172,
"gnomad_genomes_ac": 68,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005295932292938232,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.023,
"revel_prediction": "Benign",
"alphamissense_score": 0.088,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.97,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.616,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001303512.2",
"gene_symbol": "PDZD4",
"hgnc_id": 21167,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1559C>G",
"hgvs_p": "p.Pro520Arg"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}